RasMol is a program for molecular graphics visualisation originally
developed by Roger Sayle. This site is provided for the convenience
of users of RasMol and developers of open source versions of
RasMol. The site itself is provided courtesy of Bernstein + Sons.
Maintenance of RasMol, much of the development, and integration
of modifications provided by the community is done at the
ARCiB project at RIT. For the convenience of
contributors to the RasMol project, an open source collaborative
development site is used:

Work on RasMol has been supported in part by grants from the U.S. Department of Energy,
the U.S. National Science Foundation and the U.S. NIH National Institute of General Medical Sciences.
Any opinions, findings, and conclusions or recommendations expressed in this material are those of
the author(s) and do not necessarily reflect the views of the funding agencies.

User support in the form of donations will help us to
continue the development of RasMol. Registration will help us to keep you posted
on new versions.

In order to ensure continuing availability of source code and
documentation most programs and documents on this site
are subject to copyright. This does not prevent you from using
the open-source versions of RasMol, from making copies and changes,
but prevents the creation of "closed source" versions
out of the open source versions. Appropriate copyrights and licenses
appear with the relevant sources and documents. See
Copyright and NOTICE
for applicable Copyright and other Notices.

Welcome to the RasMol and OpenRasMol web site. This site was established
in
mid-September 2000 to provide a home for developers of Open Source
versions of
RasMol. In May 2002, it also became a home page for users of RasMol.
RasMol is
an important scientific tool for visualisation
of molecules created by Roger Sayle in 1992. RasMol is used by
hundreds of thousands of users world-wide to view macromolecules
and to prepare publication-quality images. Science is best served
when the tools we use are fully understood by those who wield those
tools and by those who make used of results obtained with those tools.
When a scientific tool exists as software, access to source code is
an important element in achieving full understanding of that tool.
As our field evolves and new versions of software are required,
access to source allows us to adapt our tools quickly and effectively.

There has always been free access to the source of the main line
of RasMol development. With the creation of the RasMol 2.7 series
of releases starting in 1999, RasMol formally became an open source program.
There is some confusion about the meaning of the phrase
"open source". In the early days of software development,
most scientific software source code was freely and openly shared with a
minimum of formalities. These days, it appears that carefully drawn
legal documents are necessary to protect free access to the source
code of scientific software. We are all deeply indebted to
Richard Stallman for showing
us how a creative combination of copyrights and seemingly restrictive
licenses could give us truly unfettered freedom to use programs,
to read their source code and to develop new versions. The
GNU project, and the
Linux project have shown that
an open source approach works. Until the RasMol 2.7.3 release, we
had not used the GNU General Public License
(the "GPL")
for OpenRasMol in the past, but the OpenRasMol conditions
for use have correctly been called "GPL-like"
and starting with RasMol 2.7.3, RasMol may now be distributed
under the GPL. In view of the increasing used of GPL'd packages
to support new features in RasMol, it is best to use the GPL for
all versions from RasMol 2.7.3 onwards. This is certainly the
case for binary releases from RasMol 2.7.5 onwards.

You can find a complete explanation of the OpenRasMol conditions for
relases prior to the 2.7.3 release (RASLIC)
in the page on Copying and Distribution.
If you are a user of OpenRasMol programs, you will find that
the copyrights and notices ask little more of you than that you
avoid mistakes by others by keeping the notices with copies,
display scientific integrity by citing your sources properly and
treating this like other shared scientific developments by not
inferring a warranty. If you are a software developer and wish to incorporate what you
find here into new code, or to pick up bits and pieces and used them
in another context, the situation becomes more complex. Read the
copyrights and notices carefully. You will find that they are
"infectious". Whatever you make from our Open Source code
must itself be offered as Open Source code. In addition, in
order to allow users to understand what has changed and to ensure orderly
development you have to describe your changes.

To avoid any misunderstanding -- please note that when you contribute to
RasMol by making changes and contributing code, you do not
acquire a copyright in the program as a whole. We are delighted to
acknowledge each author who contributes and to recognize their
copyright from the moment of creation in their modifications, but
once they make those modifications a part of RasMol to make what
is called a "derived work" the resulting work is under the copyrights
of Roger Sayle and Herbert Bernstein. This is necessary so that
in the future we can have the option of ensuring that the open source
licenses can be continued by transferring the copyright to another
organization.

IMPORTANT NOTE:Future releases of RasMol will continue to
offer the GPL and RASLIC as alternative licenses for the source
code, but, in order to conform to the license conditions of
various libraries to which executables may be linked, starting with
RasMol 2.7.5 release, the
GPL is the only valid license to use the binary distributions.

There is a lot still to be done before this site is fully functional.
Many links and features need to be added.
With your help, with your comments, suggestions and corrections,
and with contributions of new Open Source RasMol code and documentation,
hopefully this site will evolve into an increasingly useful tool
for the community.

RasMol is a molecular graphics program intended for the visualisation of
proteins, nucleic acids and small molecules.
The program is aimed at display, teaching and generation of
publication quality images. RasMol runs on wide range of architectures
and operating systems including Microsoft Windows, Apple
Macintosh, UNIX and VMS systems. UNIX and VMS versions require an 8, 24 or
32 bit colour X Windows display (X11R4 or later). The X Windows version of
RasMol provides optional support for a hardware dials box and accelerated
shared memory communication (via the XInput and MIT-SHM extensions)
if available on the current X Server.

The program reads in a
molecule coordinate file and interactively displays the molecule on the
screen in a variety of colour schemes and molecule representations. Currently
available representations include depth-cued wireframes, 'Dreiding' sticks,
spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular
ribbons, atom labels and dot surfaces.

The X Windows version of RasMol provides optional support for a
hardware dials box and accelerated shared memory communication (via
the XInput and MIT-SHM extensions) if available on the current X Server.

The program reads in molecular coordinate files and interactively
displays the molecule on the screen in a variety of representations
and colour schemes. Supported input file formats include Protein
Data Bank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats,
Molecular Design Limited's (MDL) Mol file format, Minnesota
Supercomputer Center's (MSC) XYZ (XMol) format, CHARMm format,
CIF format and mmCIF format files. If connectivity information is
not contained in the file this is calculated automatically. The
loaded molecule can be shown as wireframe bonds, cylinder 'Dreiding'
stick bonds, alpha-carbon trace, space-filling (CPK) spheres,
macromolecular ribbons (either smooth shaded solid ribbons or parallel
strands), hydrogen bonding and dot surface representations. Atoms
may also be labelled with arbitrary text strings. Alternate conformers
and multiple NMR models may be specially coloured and identified in
atom labels. Different parts of the molecule may be represented and
coloured independently of the rest of the molecule or displayed in
several representations simultaneously. The displayed molecule may
be rotated, translated, zoomed and z-clipped (slabbed) interactively
using either the mouse, the scroll bars, the command line or an attached
dial box. RasMol can read a prepared list of commands from a 'script'
file (or via inter-process communication) to allow a given image or
viewpoint to be restored quickly. RasMol can also create a script file
containing the commands required to regenerate the current image. Finally,
the rendered image may be written out in a variety of formats including
either raster or vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile
or as a MolScript input script or Kinemage.

The RasMol help facility can be accessed by typing "help <topic>" or "help
<topic> <subtopic>" from the command line. A complete list of RasMol commands
may be displayed by typing "help commands". A single question mark may also
be used to abbreviate the keyword "help". Please type "help notices" for
important notices.

The preliminary release of RasMol 2.7.2,
made the following changes to RasMol 2.7.1:

Incorporation of some of the code from the UCB RasMol variants.
Out thanks to Eileen Lewis and Marco Molinaro for their cooperation
in contributing the UCB Enhanced RasMol code for incorporation
into the RasMol 2.7 series.

Code to represent bonds in and to alternate conformers with
a narrowed portion in the middle of each bond.

An attempt to fix some of the chirality reversals in some of the
output modes.

Fixes for some of the problems reported since the last release.

This release does not include the toolbar from the UCB mods. In order
to resolve some cross-platform issues we have started incorporation of
the UCB code for multiple molecules and bond rotation by adding to
the command interface and to the menus. We expect to be able to
add a toolbar in a future release.

This release is not fully debugged and has some serious problems. This
release is intended for testing and experimentation and not for
production use. Comments and suggestions would be appreciated. We
are aware fo the following deficiencies:

RasMol may have difficulty in allocating colours for molecules
after the first. The fix for this interacts with some other
pending changes, and should be ready for the next release.

As has been true for all recent versions, the stereo mode defaults
to cross-eyed, which is inconvenient for many users. The next release
will allow cross-eyed and wall-eyed stereo to be selected from the menus.

Printing under windows is not working for many modern systems.
We hope to have a fix for the next release.

The fixes for several of the bugs reported against RasMol 2.7.1 have
not been incorporated into RasMol 2.7.2 yet. Our apologies. If you
previously reported a bug in RasMol 2.7.1 which still exists in 2.7.2,
you may resubmit your report, but there is no need to do so.

The release of RasMol 2.7.2.1
made the following changes to RasMol 2.7.2, incorporating changes from
RasMol 2.7.1.1 and some changes from RasTop 1.3:

Adaption of the multilingual mods from RasMol 2.7.1.1 into Rasmol 2.7.2.1.

Rewrite of the mouse handling and rotation logic to correct the
problems in 2.7.2 and make the feel of 2.7.2.1
closer to that of RasMol 2.7.1.

Addition of French menus and messages

Addition of Italian menus and messages

Adoption of picking for selection of atoms, groups or chains from
RasTop 1.3.

Adoption of backclipping from RasTop 1.3

Adoption of shadepower command for glassy surfaces from RasTop 1.3

Change of the menu stereo option to rotate cross-wall-none

Allow longer atom names (12 characters) in CIFs.

This release should hopefully represent a move toward stability for
the 2.7.2 versions. However, in order to allow for prompt release of the
French and Italian versions, some pending corrections have not yet been
integrated. Comments and suggestions appreciated.

The 2.7.2.1.1 release is the final reference release for the 2.7.2 series prior to the
creation of version 2.7.3. For most users
there should be no operational changes from version 2.7.2.1, except for the correction to the loading of PDB exchange
dictionary CIFS.

Note: Patches to command.c were included to fix the handling of load inline in the UCB multiple
molecule environment. In addition conditional code controlled by STRICT was disabled to restore operation of load inline
under windows. Thanks to Jan Reichert
jr@imb-jena.de
for pointing out these problems. Thanks to E. Martz
emartz@microbio.umass.edu
for pointing out an error in the Spanish translation credits which has been corrected.

The 2.7.3 release is the initial release of the 2.7.3 series. This release
includes the base level of code for software rendering of Lee-Richards molecular
surfaces, and is intended to provide a stable base for hardware-assisted rendering of
molecule surfaces in future releases, and for other changes. Work on RasMol 2.7.3
has been supported in part by grants DBI-0203064, DBI-0315281 and EF-0312612 from the
U.S. National Science Foundation and grant DE-FG02-03ER63601 from the U.S. Department of
Energy. This release has been in alpha test since February 2005 and is believed to now
be ready for beta test. There are major additional changes pending to be applied
once this base level is stable, including further molecular surface code and
code to apply crystallographic and non-crystallographic symmetry. This release
may be distributed under the GPL.

This release is based on
RasMol
2.7.2.1.1,
the final reference release for the 2.7.2 series. The changes for the
2.7.3 release include:

Adjustment to the mouse handling for a better, more natural feel. Our thanks
to C. Chigbo for the suggestion.

Correction to cif.c for blanks after an initial quote mark.
cif.c.patch

Correction to mswin31.c to restore lost initializations of ZRange
and DialValue[8..9].
mswin31.c.patch

Revision to CPK colors by C. Chigbo.
cpknew.patch.
The new colors are called CPKNEW. The current CPK colors remain available
as CPK. (Revised 16 Jan 2005 by HJB).

Correction to negative torsion angle monitors and to
imprecise distance and angle monitors by C. Chigbo. datconsis.patch.
(Revised 16 Jan 2005).
This patch corrects the display of negative torsion angles caused by use of
the unsigned short type, and correctys imprecise distance and angle displays.
This extends the original patch which was just for torsion angles (torsion.patch).
A side effect of this change is to limit the available range for distance monitors
to approximately 327 Ångstroms.

Initial code for display of solid Lee-Richards molecular surfaces. surface3.patch.
(Rev 20 Jan 05).
This patch adds the basic code for display of Lee-Richards surfaces with a
new Molecular Surface menu item, and surface molecule <probe
radius> and
surface solvent <probe radius> commands. Two other, related, major
patches
are pending that depend upon this one: code by P. Zhivkov to simulate
surfaces efficiently by blurring and code to display surfaces using OpenGL.

Corrections of ribbons 0, etc. commands by R. Chachra. comb3.patch.
(Revised 18 Jan 05).
With this patch, the wireframe 0, ribbon 0, cartoon 0,
backbone 0, strands 0 and trace 0 commands work the same as
these
command with off instead of 0.

Support for maps. On systems with sufficient memory, RasMol now can
read maps in CCP4 and CBF map formats and can write maps in CBF map
format. Maps of density from pseudo-Gaussian atoms can be generated.
Support is provided for generation of surfaces for SAXS bead models.

An MS windows installer was proposed by G. A. Pozhvanov, and reimplemented
on the open source base of NSIS-2.21.

A unix installer script, rasmol_install.sh, and a matching script
to select an appropropriate binary version to run under unix, rasmol_run.sh
have been added by H. J. Bernstein

In response to a bug report from Steve Shaw (shaws at mail dot nih dot gov) at the NIH, two new
options have been added for export of VRML images: "rotate"
and "mirror".

write vrml mirror <filename>

will write a vrml file with all axes mirrored (x -> -x, y -> -y
and z -> -z) and

Code from 2003 by Vencislav Stanev to export Raster3D scripts
from RasMol was integerated with this release, and support for
ribbons was added.

In order to support builds on newer 64-bit unix systems, Nikolay
Darakev added code to the build scripts to check the length of
long integers and to adjust the builds.

Other Corrections and improvements:

Fix torsion angle calculation as per bug report and patch by Swati Jain.

Corrections by Ladislav Michnovic to port to more platforms.

Code to read remediated PDB entries as suggested by Huanwang Yang.

Updated icons.

Extended export menus.

Alignment of command line sizing and positioning options for Windows and X-Windows version. The command line options -height nnnn, -width
nnnn, -xpos nnnn and -ypos nnnn may be used to set the size and position of the initial window.

Change of the encoding for Japanese messages and menus from SJIS to EUC-JP, and corrections to the fontset handling for Chinese and Japanese.
Thanks to Mamoru Yamanishi for contributing the improved fontset logic.

Updates to the rasmol_install.sh and rasmol_run.sh scripts to support Chinese and Japanese using cxterm.

Optional use of GTK. Thanks to Teemu Ikonen for the new GTK code.

The svn at http://sf.net/projects/openrasmol should be consulted for details
of
the code changes.

The Unix version of RasMol supports decompression of compressed data
files using pipes.
Mamoru Yamanishi has prepared modifications for RasMol 2.7.2.1 to support
use of decompression using the zlib (http://www.gzip.org/zlib) library, which
should allow decompression of compressed data files on non-Unix platforms.
These new modifications are being studied for inclusion in a future RasMol
standard release for use on systems for which a pipe to a standard
decompression utility is not practical to use. The source code mods to
RasMol 2.7.2.1 for use of zlib under Mac OS are available for testing.

RasTop is a
graphical interface to RasMol adapted for Windows platform,
i.e. RasTop is a GUI front end for RasWin.

RasTop offers a user-friendly graphical interface around
"RasMol molecular engine". No more typing on the command line;
each command in the menu generates its own script that is
transferred to RasMol. RasTop has numerous extensions to handle
atom selections: addition and subtraction of atoms, groups, or
chains, selection on screen with a lasso, ability to go back
to the previous selection, copying to and pasting selections
from the clipboard, new set operations such as inverse,
extraction, summation, subtraction, and exclusion, and finally
full saving of all user-defined atom sets under an extended script
format called RSM script.

During its development, a few new capabilities were added: back
clipping, 32-bit output under Windows, full centring command
either on a selected atom or to the origin, variation of depthcue
in slab mode, and a colouring command, shadepower, which
generates new metal-like surfaces.

RasTop allows several molecules to be opened at the same time
(on different windows) and provides limited editing of the
molecular file.

RasTop 1.3, like RasMol 2.7.1, contains a lot of new code.
Under its current version, RasTop 1.3 has been extensively
tested with molecular files in pdb format and showed good
stability. Nevertheless you should be careful in testing
other formats.

This is a minor update with modifications concerning mainly correction of bugs
reported for the 1.3 version. The software is
now supported under Windows 2000
operating system. The software seems also stable under Windows ME. A release for
8-bit monitors is also available (although never tested on a true 256
colors monitor). A few systems are missing an updated version of the mfc42.dll
file which is also available, but requires separate installation.

Operationally, there are very few changes. Maybe the most interesting for rasmol is
the use of white color for carbon atoms when there are no hydrogen on the molecule
on opening. The squareroot calculations for drawing ribbons at large zoom have
been corrected.

RasTop 2.0 is a user-friendly graphical interface build on top of RasMol
(version 2.7.2.1) available for Windows platforms. This is a major update
over the 1.3.1 version. The interface now accepts multiple molecules. It
has
high color resolution and improvement of the rendering (depth queuing,
multidirectional headlight, new cylinder code, better ribbons). The
Richards - Connolly surfaces are now complete. A script can be started
automatically on molecule opening.

Comments, suggestions, and bug reports will be extremely appreciated. The
immediate goal is to obtain stable multiple molecule environment and
compatibility with recent versions of Windows.

RasTop 2.1 is a user-friendly graphical interface build on top of RasMol
available for Windows platforms.

In the RasTop 2.1 release "numerous bugs have been corrected ...
A command
window similar to the one in the original RasMol program has been added. This feature was
requested by numerous teachers and was initially developed by Christian Duque. RasTop is
now localizable to multiple languages, see RasTop help. A 'scripting' toolbar has been
added to improve the handling of scripts. Scripts located in the "rastop/scripts" folder
are directly accessible on the new toolbar. Images can be saved as bmp files in 32-bit
format.